In the summer before her freshman year of high school, Melinda Sordino was physically assualted at a party by a popular senior, Andy Evans. Melinda calls the police and they break up the party. When those attended the party find out that it was Melinda who called the police, even her closest friends refuse to speak to her and Melinda begins her freshman year as an outcast, friendless except for a new student, Heather, who Melinda refers to throughout the first part of the novel as 'Heather from Ohio'. Heather constantly asks Melinda for help on things but never defends Melinda from a clique she wants to join called "The Marthas". Heather soon dumps Melinda the clique. Throughout the year, Melinda fails classes and skips school and classes as a result of the depression from her self-blame. All of her teachers dislike her, except Melinda's art teacher, Mr. Freeman, who asks his students to focus on one randomly chosen topic and make it "say something" by the end of the year. Melinda is assigned the subject "tree." She isn't too thrilled and thinks it will be easy, but later finds a challenge in her project.

Over the course of the year, Melinda works to regain some confidence and regain her former friendships. The development of her tree artwork mirrors her gradual regrowth. When one of her former friends, Rachel, begins dating Andy Evans, Melinda works up the courage to begin telling her story, if only in fragments. At the close of the novel, Andy confronts her, telling her that she lied about the assault, he had not hurt her and that she asked for it. He suggests that jealousy of his relationship with Rachel was her motivation for "lying" about the rape and attempts to assault her again. She breaks a mirror and holds a shard of glass up to his neck. "I SAID NO!" she yells. This is a major turning point for her, as one of the issues factoring into her silence and self-blame was that she was in shock, and couldn't say no. One of Melinda's former friends from the eighth grade, Nicole, and the rest of the lacrosse team, then break into the closet Melinda was cleaning out when Andy tried to hurt her and help Melinda out.

The truth comes out about what happened at the party. Realizing the truth, the students no longer treat Melinda as an outcast but as a sort of hero instead. And finally, Melinda tells her story to her art teacher, Mr. Freeman. And the truth finally sets her free. Her best friend who was dating the Andy, broke up with him on prom night. As Melinda was going about school days, her disguise used to make her stay in her own world alone, soon began to break apart as she got closer, to "Speak."